There’s a new paper out on Amerindian genetic history in Science,mostly looking at 92 ancient mitochondrial genomes (500 to 8600 years old). Because mtDNA has a high mutation rate, it’s useful for seeing rapid changes in population size (Bayesian skyline analysis). It looks as if the Amerindian wave started about 16k years ago, first down the Pacific coast, since this was before the ice-free passage across the Rockies opened up.

There is that weird Andaman-like signature; which they say is compatible with a second migration. They also say that it might have come later, but looking at the distribution, that’s impossible. There’s no way to come in later and end up spread out at the 2% level all across the Amazon. More later.

They see clear evidence of a big population expansion after the move into the Americas – of course that makes sense.

People don’t seem to have moved around too much after the initial settlement. No big expansions like you see in the Old World.

Now for the weirdness. None of the ancient DNA samples have any descendants or close relatives today. Zip. “no ancient haplotype shares a common ancestor with a modern haplotype more recently than ~9,000 years ago. Their samples were mostly taken from large population centers along the western coast of South America: apparently those people went extinct after Columbus. The model that best fit their data was the following:

“Model C also assumes one panmictic population of constant size (2,000 females), and the same growth between 500–600 generations ago as in Model A. Following the massive increase in Ne we assumed a split into two demes (0 and 1) of equal size (50,000 females each with no migration between demes) around 360 generations ago (~9,000 years ago or the last time we observe an ancestor common to modern and ancient lineages in hg A2; black triangle in Fig. 3B), and a constant population size for both (‘geographically’) isolated demes. Ancient lineages were exclusively sampled from deme 1 by converting radiocarbon or archeological dates into number of generations. To account for an extinction of ancient lineages as a consequence of the contact with European colonizers, we modeled a drastic population decline from 50,000 to 1 female (virtually extinct) for deme 1 between 20 generations ago (~1500 AD) and to the present day (time 0). In contrast, we assumed an exponential growth for deme 0 to 100,000 females over the last 20 generations to account for the present-day mitochondrial diversity. ”

They posit two distinct kind of Indians: those that left fossil DNA, and those that left descendants. Good Indians, and bad Indians.

Now it makes sense that lowland types suffered more than people in the Andean or Mexican highlands: they faced African diseases like falciparum malaria and yellow fever as well as the huge array of Eurasian diseases. And the Spanish had their own problems with altitude in the Andean highlands.

But this is nuts! or at any rate amazing. It suggests that in large areas, Amerindians went extinct, and were later replaced by different Amerindians from other places (plus Spaniards and Portuguese), not too closely related. That’s not incredibly far from what happened in the Caribbean, maybe: we know the local Indians disappeared rapidly there (although even there, they are a significant maternal component in existing populations). And there are indications that at least some of the hunter-gatherer tribes of the Amazon might be new to the neighborhood.. And maybe densely populated areas were hit hardest by the new infectious diseases, with a few of the Amerindian equivalent of hillbillies surviving…

And maybe there is undersampling of existing populations. But it sure sounds weird.

“Our ancient samples were principally derived from large population centers along the western coast of South America, which experienced high extinction rates following European colonization. Historic accounts have reported that the population decline was more rapid and intense in the Gulf of Mexico and the Pacific coast of Peru than in other areas such as the Mesoamerican plateau or the Andean highlands (7).

They didn’t just look at mtDNA. I am not concluding anything yet. This is an amazing finding and I am sure we will have opinions from Razib, Davidski, and John Hawks soon enough. What it seems to indicate is european diseases wiped out 100% of some amerindian populations.

It started with European diseases, then the diseases from Africa wiped out any survivors (at least at low altitudes). The Europeans were killed by the African diseases too. First attempt to build the Panama Canal (by the French) resulted in mass deaths from yellow fever. The Africans seemed to possess some resistance to it.

I like your hypothesis but I would state it differently. A lot of african/tropical diseases spread to Europe but some of them like falciparum malaria spread only so far north. I would guess that those amerind populations living in warm tropical locations and absolutely no genetic protection towards diseases were likely candidates to be completely wiped out. I am guessing not all amerind populations were the same in their genetic predisposition to disease resistance. Time will tell because this study is just scratching the surface if it only looked at mtDNA.

I recently commented on the James Thompson blog (http://drjamesthompson.blogspot.co.uk) that there seemed to be an odd discrepancy between the low intellectual levels of modern Amerindians, and the high culture achieved by the likes of the Incas and Aztecs. I speculated that selective death by disease after Columbus might be a cause. I’m tickled pink to think that that speculation might have had some merit.

So here’s another of my recent speculations: all the much moaned-about overtreatment with antibiotics might be once of the causes of the end of the epidemic of CVD in Western countries.

I speculated that selective death by disease after Columbus might be a cause. I’m tickled pink to think that that speculation might have had some merit.

It might simply be that the surviving high IQ Mesoamericans rapidly married into the Spanish population, the new elite. At least, there are accounts of royal Aztec and Inca maidens taking this path. I’m not sure, of course, that such civilizations were exactly as meritocratic as modern society.

The Aztecs though seemed to have been recent intruders into the Valley of Mexico from the North. Their language is Uto-Aztecan and most closely related to the languages of the Taos Pueblos and Kiowa. They were not the creators of Mesoamerican culture.

Because the Aztecs were at the height of their power at the arrival of Europeans they are often excessively associated with Mesoamerican culture but the history of Mesoamerican cultures goes back to long before the Aztecs.

One interesting difference between Mesoamerican cultures and the cultures of the Ancient Near East and Egypt is that while both cultures developed true writing systems, in the case of Mesoamerica, unlike the ANE and Egypt, knowledge of writing seems to have been restricted to a very small elite and hardly used at all in ordinary life. Knowledge of writing in the ANE and Egypt was not restricted to an elite. We have examples of graffiti in Egyptian temples written by workmen.

“the history of Mesoamerican cultures goes back to long before the Aztecs: indeed. That’s why my original comment referred to their predecessors – “(i) … the Incas, Aztecs, and their predecessors being capable of building and running advanced empires, …”

Our hosts would love that the end of the CVD epidemic was true. Unfortunately, no end is in sight in our lifetimes. But you are on to something: CVD seems to be an inflammatory disease caused by mouth bacteria.

Since you think that Native Americans can be separated thru Their IQs, even though they are the same race, more closely related to each other than any other race, it’s safe to say that since the Greeks and Romans had literacy, works of fine art, and monumental architecture, because they were Southern Europeans, that the Northern, Western, and Eastern Europeans were low IQ barbarians, who had no art, were completely illiterate, and lived in subterranean hits, and slept with their pigs to keep warm. And would of stayed like that, happily, until they were pulled out of their squalor by their conquerors, the Romans, who though European, are Genetically different but Obviously superior to the rest of The European People. Since you think that having Art, Litteracy and monumental structures proves intellectual superiority, that the North American Indians have higher IQs than most of Europeans, and thus, superior to your ancestors, also you are forgetting Cahokia, the Mound Builders, and the Anazasi the Pueblo builders. You also forget the Roman and Greeks fell into the dark ages. I guess their IQs dropped from inter breeding with the Vandals, Celts, Gauls, Silurians, Brittons, Angles, Saxons, Germanics and all the other Low IQ tribes of Europe.

Who knows. But occupation was continuous. Anyhow, the samples weren’t taken from highland areas like Potosi: recorded history makes it clear that the population collapse was less bad at higher altitudes.

Extreme, but not inconceivable. Mexican migrants to the US today are highly Indian genetically, but of course a Mexican in, say, Chicago is not related to the Indians who used to live there. Someday someone may look at the US and say, “Looks like there were Indians, then this interlude of white people, then Indians a gain–but weirdly, they’re totally different Indians,”

How much does the percentage of Amerindian ancestry in Mexican migrants to the US today differ from the average of the Mexican population? Are the migrants coming more from the south of Mexico where Amerindian ancestry is higher?

Indians with agriculture and states are kind of immobile and densely settled. Get wiped out by diseases. Suppose there are other indians who live in isolated family groups in wild places and kill strangers on sight. Less exposure to disease, able to evolve resistance rather than perish totally. Absorb some white resistance genes.

Statelike indians live in the more productive places, conquerors hit them hard. Start abducting replacement indians from the wild places. Plausible that every single existing Indian is descended from the wild stateless indians. Plausible that wild stateless Indians have burial practices that mean that bones are hard to find or get destroyed.

Spanish Colonial administration in the Alto Peru (= Bolivia) was 80-90% financed by head tax on the settled, organized Quechua communities. The system caused the registered Indians to escape and avoid paying the tax and the yearly mita de Potosi service, reducing the administration’s tax basis. 400 years of Spanish grinding and wearing down left little of the Pre-Columbian peoples.

So, let’s try to regroup and look at the big picture. I’m going to list all the known and suspected migrations into the Americas. Correct me where I’m wrong.

The Andaman-like people, whose existence was only recently discovered due to the paucity of genetic and archaeological remains. Therefore, their time and route of entry into the Americas is very mysterious. They are almost gone but have left a small signature in modern-day Amazonians.
The group discussed in this latest paper, who were trapped in Beringia for a few thousand years. They then migrated into the Americas and quickly increased in number about 16,000 years ago. Those who survived the Columbian Exchange form the majority of modern South American native DNA.
Clovis? Although I have not finished the paper, my biggest question is where Clovis now fits into things–the former explanation, that it was the first group of people to settle the Americas, nicely explained the lack of cultural diversity over such a large area. And supposedly Clovis closely matches modern Native North Americans, insofar as they have been sampled. Is Clovis extremely closely related to group #2, and represents some kind of expansion of people already in the continent (like Pama-Nyungan languages in Australia), or were they a separate migration that came later?
Na-Dene people–came from Siberia several thousand years ago, and left a distinctive genetic signature in people who speak these languages today.
The Thule, predecessors of the Inuit.
The Inuit, who arrived about 700 years ago and seem to have wiped out the the Thule.

Whew! This is starting to look much more complicated than people once believed, and that the levels of Native genetic diversity would imply. This must be because all people in the Americas prior to 1492 (except maybe for the Andamanish folk) came from the same area of Siberia, and hence none of the source populations were very genetically distant. Getting to the bottom of this story will be fascinating.

Probably the rapidly expanding population at 16,000 years ago stayed close to water for a long time. Clovis was successful because their new technology let them take full advantage of the large inland mega-fauna. They look like a local development genetically.

News in SoCal is the little girl who was taken away from the family that wanted to adopt her because she is Native American, and so has to be raised by a Native American family. She is 1/64 Choctaw. That’s less than 2% Native American. But think how devastating it would be to a child who is 63/64 non Native American to be raised in a non Native American home!

So just to be clear they are saying the Adaman looking admixture is later because that’s politically correct and acceptable? It just wouldn’t do to have the current Natives wiping out the previous natives.

Bullshit, they didn’t say that adamese islanders settled the Americans , not first, not at all. It said that it came later with the Aleutians, who also have the signature, Aleutians are latecomers to the Aleutian Islands. And that it is Australasian-Like, not Adamanese! Besides that, if it was in America from the start, all Native Americans would have it at the same levels, not just a few Amazonian tribes. As the article says, it was the Europeans who commited mass genocide on the Native Americans, 50,000 to 1, a near complete genocide. Know one else in the history of this planet, has there been any other genocide that even comes close to the near destruction of a race of people, it’s disgusting that you are trying throw of the sins of the Europeans and pin them on the Victims of a real genocide.

The Amerindian population collapsed because of the Old World diseases, not because of fighting. ” 50,000 to 1 ” – what can that possibly mean?

And the most plausible explanation of the new genetic results showing an Andamanese-like admixture in Amerindians – only in South America – is that the Andamanese-like population got there first. There were two papers talking about this: one is technically better than the other.

I read somewhere the number of ppl killed by the Mongol conquest of China wasn’t just the direct casualties but famines etc caused by the reduced numbers being unable to maintain their complex irrigation systems etc.

So maybe 90% HGs die from a plague but individual survivors can survive alone until reform a group but 90% of a complex farmer society dies from a plague and the survivors can’t survive on their own and so die off for other reasons?

The very big hole in all these studies is the US. US Indians and US law will not permit genetic studies of either the living tribes or of the fossils. Until we get some DNA data from the US tribes, we’re not going to understand what happened.

Usually Amerindian genomes are carefully selected from unadmixed or minimally admixed individuals as much as possible. A reduction in population by say 90%, followed by assimilation with European settlers by 99%, is well within the range of possibility and might cause mtDNA haplogroups with which ancient mtDNA has a common ancestor to not appear in existing datasets.

The contemporary samples all have mtDNAs from known Amerindian haplogroups. They’re not European. Moreover, in the cases we know anything about, mixed populations tend to have more Amerindian mtDNA vs more European Y-chromosomes.

In this case the source for the modern mitogenomes included a lot of mixed populations, not just indios. Eyeballing the map I guess the places where the samples came from are presently fairly mestizo. However, most of the ancient samples were from Peru, while the modern samples were from all over the place, with only a small proportion from Peru – a total of 11, plus any relevant ones on PhyloTree. I don’t see anything about comparing with the much larger database of partial sequences out there. So I don’t suppose anything rules out these lineages still existing at low frequency.